Technical Abstract:
Weedy rice is a persistent weed of cultivated rice (Oryza sativa) fields worldwide, which competes with the crop and drastically reduces rice yields. Within the US, two main populations of genetically differentiated weedy rice exist, the straw-hulled (SH) group and the black-hulled awned (BHA) group. Current research suggests that both groups are derived from Asian cultivated rice, such that SH weeds are most closely related to a rice variety called indica, while the BHA group is more closely related to a variety known as aus. However, the weeds differ from the cultivated groups in various morphological traits. Flowering time is one trait where consistent differences are seen between weedy rice and cultivated rice, and timing of flowering is expected to be important for persistence of weeds in the field. Recently, it has been suggested that the coding region of hd1 and the promoter of hd3a are two of the three most important determinants of flowering time in cultivated rice. In order to determine whether these genes have been mutated in weedy rice so as to cause aberrant flowering phenotypes we took a phenotypic and candidate gene approach. We measured flowering time in cultivated, weedy and wild rice grown in a growth chamber under day neutral conditions, and we sequenced the entirety of the hd1 gene along with the promoter of the hd3a gene. We show that SH weeds flower significantly earlier than cultivated rice while BHA weeds flower slightly later than most cultivated rice. All later flowering BHA samples share a 2 base pair (bp) deletion in exon 2 of the hd1 coding region that is common in tropical japonica and aus cultivars, yet is also found in some indica cultivars. While the 2 bp deletion differentiates BHA from SH weeds, it does not differentiate the weeds from their putative progenitors. Additionally, nearly all SH and BHA weeds share hd3a promoter haplotypes with their respective progenitors, indica and aus cultivars.